In India, crossbred cows incorporate the high production of dairy breeds and the environmental adaptation of local cattle. Adaptation to different environments and selection in milk production have shaped the genetic differences between and cattle. The aim of this paper was to detect, for milk yield of crossbred cows, quantitative trait loci (QTL) that differentiate from ancestry, as well as QTL that are segregating within the ancestral breeds. A total of 123,042 test-day milk records for 4,968 crossbred cows, genotyped with real and imputed 770 K SNP, were used. Breed origins were assigned to haplotypes of crossbred cows, and from that, were assigned to SNP alleles. At a false discovery rate (FDR) of 30%, a large number of genomic regions showed significant effects of versus origin on milk yield, with positive effects coming from both ancestors. No significant regions were detected for Holstein Friesian (HF) versus Jersey effects on milk yield. Additionally, no regions for SNP alleles segregating within indigenous, within HF, and within Jersey were detected. The most significant effects, at FDR 5%, were found in a region on BTA5 (43.98-49.44 Mbp) that differentiates from , with an estimated difference between homozygotes of approximately 10% of average yield, in favour of origin. Our results indicate that evolutionary differences between and cattle for milk yield, as expressed in crossbred cows, occur at many causative loci across the genome. Although subject to the usual first estimation bias, some of the loci appear to have large effects that might make them useful for genomic selection in crossbreds, if confirmed in subsequent studies.